FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JL249

Calculation Name: 3QHY-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QHY

Chain ID: B

ChEMBL ID:

UniProt ID: O87916

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 271
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3184028.200369
FMO2-HF: Nuclear repulsion 3089965.898555
FMO2-HF: Total energy -94062.301814
FMO2-MP2: Total energy -94342.933951


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:41:ALA)


Summations of interaction energy for fragment #1(B:41:ALA)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-27.402-18.4449.916-6.776-12.094-0.045
Interaction energy analysis for fragmet #1(B:41:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.020
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3B43SER0-0.046-0.0193.005-0.8300.9990.022-0.857-0.9950.005
4B44VAL00.0520.0342.947-2.433-1.1130.234-0.612-0.942-0.006
5B45VAL0-0.064-0.0245.2350.2590.258-0.001-0.0010.0040.000
6B46ALA00.0360.0298.504-0.071-0.0710.0000.0000.0000.000
7B47TRP0-0.055-0.04410.5780.0570.0570.0000.0000.0000.000
8B48GLY00.0180.01114.792-0.015-0.0150.0000.0000.0000.000
9B49GLY00.0320.00918.190-0.002-0.0020.0000.0000.0000.000
10B50ASN0-0.081-0.05420.899-0.002-0.0020.0000.0000.0000.000
11B51ASN0-0.0100.00017.8930.0030.0030.0000.0000.0000.000
12B52ASP-1-0.834-0.90820.414-0.047-0.0470.0000.0000.0000.000
13B53TRP0-0.042-0.02121.1910.0100.0100.0000.0000.0000.000
14B54GLY0-0.016-0.00418.7020.0100.0100.0000.0000.0000.000
15B55GLU-1-0.774-0.90116.387-0.091-0.0910.0000.0000.0000.000
16B56ALA0-0.0050.01013.984-0.035-0.0350.0000.0000.0000.000
17B57THR0-0.060-0.02813.999-0.010-0.0100.0000.0000.0000.000
18B58VAL00.0340.0317.7810.0200.0200.0000.0000.0000.000
19B59PRO00.0370.02710.9510.0470.0470.0000.0000.0000.000
20B60ALA00.039-0.01110.1430.0450.0450.0000.0000.0000.000
21B61GLU-1-0.874-0.9269.5430.5720.5720.0000.0000.0000.000
22B62ALA00.0070.0067.1220.2800.2800.0000.0000.0000.000
23B63GLN0-0.022-0.0105.958-0.223-0.2230.0000.0000.0000.000
24B64SER00.001-0.0063.588-0.881-0.5150.003-0.135-0.2340.000
25B65GLY0-0.029-0.0062.731-4.275-3.1871.787-1.257-1.6170.011
26B66VAL0-0.054-0.0182.520-3.677-3.9601.1270.954-1.7970.001
27B67ASP-1-0.862-0.9432.259-10.051-8.4924.489-2.829-3.219-0.039
28B68ALA0-0.011-0.0164.631-0.0490.028-0.001-0.006-0.0690.000
29B69ILE0-0.027-0.0265.6520.2020.2020.0000.0000.0000.000
30B70ALA00.0030.0208.696-0.008-0.0080.0000.0000.0000.000
31B71GLY0-0.014-0.02112.4980.0420.0420.0000.0000.0000.000
32B72GLY00.0730.03514.7620.0050.0050.0000.0000.0000.000
33B73TYR0-0.125-0.07718.2860.0000.0000.0000.0000.0000.000
34B74PHE0-0.031-0.01820.8630.0040.0040.0000.0000.0000.000
35B75HIS0-0.028-0.01817.2740.0190.0190.0000.0000.0000.000
36B76GLY00.0500.03813.313-0.029-0.0290.0000.0000.0000.000
37B77LEU0-0.014-0.01112.3170.0620.0620.0000.0000.0000.000
38B78ALA00.006-0.0147.053-0.093-0.0930.0000.0000.0000.000
39B79LEU0-0.0300.0137.8870.1570.1570.0000.0000.0000.000
40B80LYS10.8660.9136.419-2.074-2.0740.0000.0000.0000.000
41B81GLY00.0000.0157.1580.0540.0540.0000.0000.0000.000
42B82GLY0-0.0140.0029.071-0.022-0.0220.0000.0000.0000.000
43B83LYS10.8440.91710.976-0.359-0.3590.0000.0000.0000.000
44B84VAL00.0270.01011.218-0.002-0.0020.0000.0000.0000.000
45B85LEU0-0.068-0.0308.9400.0550.0550.0000.0000.0000.000
46B86GLY00.0570.00212.437-0.069-0.0690.0000.0000.0000.000
47B87TRP0-0.124-0.0609.2050.0690.0690.0000.0000.0000.000
48B88GLY00.0670.03915.501-0.029-0.0290.0000.0000.0000.000
49B89ALA0-0.007-0.00318.4300.0180.0180.0000.0000.0000.000
50B90ASN0-0.006-0.00622.012-0.017-0.0170.0000.0000.0000.000
51B91LEU0-0.035-0.01923.0430.0060.0060.0000.0000.0000.000
52B92ASN00.010-0.00824.961-0.003-0.0030.0000.0000.0000.000
53B93GLY00.0340.03424.8640.0000.0000.0000.0000.0000.000
54B94GLN00.0470.01920.4950.0170.0170.0000.0000.0000.000
55B95LEU0-0.019-0.01016.748-0.005-0.0050.0000.0000.0000.000
56B96THR0-0.077-0.03319.8710.0200.0200.0000.0000.0000.000
57B97MET0-0.0020.02515.655-0.016-0.0160.0000.0000.0000.000
58B98PRO00.0680.04520.2470.0140.0140.0000.0000.0000.000
59B99ALA00.0220.01620.7860.0050.0050.0000.0000.0000.000
60B100ALA0-0.010-0.00320.8000.0130.0130.0000.0000.0000.000
61B101THR00.004-0.02116.9250.0000.0000.0000.0000.0000.000
62B102GLN0-0.040-0.02515.9280.0170.0170.0000.0000.0000.000
63B103SER0-0.025-0.01614.9720.0360.0360.0000.0000.0000.000
64B104GLY00.0210.01214.724-0.022-0.0220.0000.0000.0000.000
65B105VAL0-0.0370.00313.643-0.017-0.0170.0000.0000.0000.000
66B106ASP-1-0.847-0.93512.700-0.149-0.1490.0000.0000.0000.000
67B107ALA0-0.022-0.01812.557-0.085-0.0850.0000.0000.0000.000
68B108ILE0-0.045-0.02310.0960.0710.0710.0000.0000.0000.000
69B109ALA00.0330.01314.066-0.045-0.0450.0000.0000.0000.000
70B110ALA0-0.017-0.01516.0370.0310.0310.0000.0000.0000.000
71B111GLY00.0810.05917.929-0.012-0.0120.0000.0000.0000.000
72B112ASN0-0.051-0.04320.862-0.009-0.0090.0000.0000.0000.000
73B113TYR00.000-0.00823.1340.0040.0040.0000.0000.0000.000
74B114HIS0-0.035-0.00222.6040.0150.0150.0000.0000.0000.000
75B115SER00.0170.00418.211-0.023-0.0230.0000.0000.0000.000
76B116LEU00.0030.00518.1640.0180.0180.0000.0000.0000.000
77B117ALA0-0.009-0.01416.823-0.022-0.0220.0000.0000.0000.000
78B118LEU0-0.0320.00916.6650.0190.0190.0000.0000.0000.000
79B119LYS10.9040.93216.830-0.016-0.0160.0000.0000.0000.000
80B120ASP-1-0.908-0.93718.964-0.020-0.0200.0000.0000.0000.000
81B121GLY0-0.0240.00020.5670.0080.0080.0000.0000.0000.000
82B122GLU-1-0.945-0.97922.237-0.037-0.0370.0000.0000.0000.000
83B123VAL0-0.002-0.00221.571-0.008-0.0080.0000.0000.0000.000
84B124ILE0-0.025-0.01920.0840.0170.0170.0000.0000.0000.000
85B125ALA00.0160.00721.319-0.014-0.0140.0000.0000.0000.000
86B126TRP0-0.060-0.04117.0400.0120.0120.0000.0000.0000.000
87B127GLY00.0110.01023.029-0.011-0.0110.0000.0000.0000.000
88B128GLY00.006-0.00724.7160.0050.0050.0000.0000.0000.000
89B129ASN0-0.013-0.02527.150-0.010-0.0100.0000.0000.0000.000
90B130GLU-1-0.970-0.97629.822-0.034-0.0340.0000.0000.0000.000
91B131ASP-1-0.812-0.88830.837-0.058-0.0580.0000.0000.0000.000
92B132GLY0-0.025-0.00531.860-0.002-0.0020.0000.0000.0000.000
93B133GLN00.024-0.01126.3740.0040.0040.0000.0000.0000.000
94B134THR0-0.011-0.01024.948-0.007-0.0070.0000.0000.0000.000
95B135THR0-0.075-0.03227.2140.0060.0060.0000.0000.0000.000
96B136VAL00.0050.02325.750-0.002-0.0020.0000.0000.0000.000
97B137PRO00.0410.03328.6870.0080.0080.0000.0000.0000.000
98B138ALA00.005-0.02030.177-0.003-0.0030.0000.0000.0000.000
99B139GLU-1-0.863-0.90330.960-0.066-0.0660.0000.0000.0000.000
100B140ALA00.0350.01826.270-0.004-0.0040.0000.0000.0000.000
101B141ARG10.8960.94226.0060.0360.0360.0000.0000.0000.000
102B142SER00.0060.00326.1060.0040.0040.0000.0000.0000.000
103B143GLY0-0.005-0.00525.768-0.001-0.0010.0000.0000.0000.000
104B144VAL0-0.060-0.00621.759-0.003-0.0030.0000.0000.0000.000
105B145ASP-1-0.840-0.92921.014-0.128-0.1280.0000.0000.0000.000
106B146ALA0-0.031-0.01718.572-0.028-0.0280.0000.0000.0000.000
107B147ILE0-0.018-0.02016.6890.0290.0290.0000.0000.0000.000
108B148ALA00.0290.02418.175-0.029-0.0290.0000.0000.0000.000
109B149ALA0-0.013-0.00519.4900.0230.0230.0000.0000.0000.000
110B150GLY00.0780.04221.074-0.011-0.0110.0000.0000.0000.000
111B151ALA0-0.057-0.02523.4970.0020.0020.0000.0000.0000.000
112B152TRP0-0.025-0.02824.9750.0010.0010.0000.0000.0000.000
113B153ALA00.0300.02325.6480.0080.0080.0000.0000.0000.000
114B154SER0-0.022-0.01623.702-0.016-0.0160.0000.0000.0000.000
115B155TYR0-0.024-0.03423.1240.0100.0100.0000.0000.0000.000
116B156ALA0-0.009-0.00622.558-0.012-0.0120.0000.0000.0000.000
117B157LEU0-0.0300.00322.1250.0080.0080.0000.0000.0000.000
118B158LYS10.8390.89723.9210.0660.0660.0000.0000.0000.000
119B159ASP-1-0.928-0.95426.355-0.075-0.0750.0000.0000.0000.000
120B160GLY0-0.0040.00926.7060.0060.0060.0000.0000.0000.000
121B161LYS10.8160.88928.1040.0700.0700.0000.0000.0000.000
122B162VAL00.0080.00526.092-0.005-0.0050.0000.0000.0000.000
123B163ILE0-0.057-0.03027.2250.0100.0100.0000.0000.0000.000
124B164ALA00.0120.00427.137-0.009-0.0090.0000.0000.0000.000
125B165TRP0-0.037-0.02625.0380.0060.0060.0000.0000.0000.000
126B166GLY00.002-0.00428.458-0.008-0.0080.0000.0000.0000.000
127B167ASP-1-0.741-0.85430.289-0.063-0.0630.0000.0000.0000.000
128B168ASP-1-0.825-0.88231.740-0.072-0.0720.0000.0000.0000.000
129B169SER0-0.092-0.05534.3800.0040.0040.0000.0000.0000.000
130B170ASP-1-0.966-0.98533.289-0.066-0.0660.0000.0000.0000.000
131B171GLY0-0.020-0.00634.756-0.003-0.0030.0000.0000.0000.000
132B172GLN00.034-0.00129.3800.0010.0010.0000.0000.0000.000
133B173THR0-0.062-0.04529.197-0.007-0.0070.0000.0000.0000.000
134B174THR0-0.053-0.02331.5900.0040.0040.0000.0000.0000.000
135B175VAL0-0.046-0.01830.534-0.003-0.0030.0000.0000.0000.000
136B176PRO00.0300.01732.0320.0060.0060.0000.0000.0000.000
137B177ALA00.022-0.00534.155-0.002-0.0020.0000.0000.0000.000
138B178GLU-1-0.833-0.91034.101-0.077-0.0770.0000.0000.0000.000
139B179ALA0-0.0020.01529.813-0.003-0.0030.0000.0000.0000.000
140B180GLN0-0.045-0.03330.445-0.001-0.0010.0000.0000.0000.000
141B181SER0-0.011-0.01531.7150.0040.0040.0000.0000.0000.000
142B182GLY00.0110.00130.141-0.001-0.0010.0000.0000.0000.000
143B183VAL0-0.045-0.01225.118-0.004-0.0040.0000.0000.0000.000
144B184THR0-0.011-0.01723.4160.0050.0050.0000.0000.0000.000
145B185ALA00.0040.00820.490-0.017-0.0170.0000.0000.0000.000
146B186LEU0-0.043-0.03120.5910.0220.0220.0000.0000.0000.000
147B187ASP-1-0.767-0.88019.479-0.244-0.2440.0000.0000.0000.000
148B188GLY0-0.0070.00721.1500.0220.0220.0000.0000.0000.000
149B189GLY00.0410.03322.077-0.012-0.0120.0000.0000.0000.000
150B190VAL0-0.078-0.05124.5270.0030.0030.0000.0000.0000.000
151B191TYR00.0280.00326.7280.0030.0030.0000.0000.0000.000
152B192THR0-0.025-0.01227.5230.0040.0040.0000.0000.0000.000
153B193ALA00.0400.03925.920-0.006-0.0060.0000.0000.0000.000
154B194LEU0-0.028-0.01623.8300.0100.0100.0000.0000.0000.000
155B195ALA00.0320.00524.776-0.008-0.0080.0000.0000.0000.000
156B196VAL0-0.0060.01723.4790.0080.0080.0000.0000.0000.000
157B197LYS10.8420.90326.1580.0820.0820.0000.0000.0000.000
158B198ASN0-0.047-0.02029.0820.0020.0020.0000.0000.0000.000
159B199GLY00.0320.02127.2330.0050.0050.0000.0000.0000.000
160B200GLY0-0.022-0.00728.3210.0000.0000.0000.0000.0000.000
161B201VAL0-0.023-0.01626.457-0.003-0.0030.0000.0000.0000.000
162B202ILE0-0.046-0.01628.6160.0100.0100.0000.0000.0000.000
163B203ALA0-0.009-0.00728.765-0.008-0.0080.0000.0000.0000.000
164B204TRP0-0.055-0.02827.6520.0060.0060.0000.0000.0000.000
165B205GLY00.0480.02730.798-0.007-0.0070.0000.0000.0000.000
166B206ASP-1-0.760-0.88932.644-0.072-0.0720.0000.0000.0000.000
167B207ASN0-0.030-0.02333.015-0.008-0.0080.0000.0000.0000.000
168B208TYR0-0.0330.00535.2310.0040.0040.0000.0000.0000.000
169B209PHE0-0.093-0.05733.1270.0040.0040.0000.0000.0000.000
170B210GLY0-0.007-0.00134.454-0.002-0.0020.0000.0000.0000.000
171B211GLN00.032-0.00729.4480.0010.0010.0000.0000.0000.000
172B212THR0-0.0020.00830.050-0.007-0.0070.0000.0000.0000.000
173B213THR0-0.043-0.00932.1990.0040.0040.0000.0000.0000.000
174B214VAL0-0.0020.01030.754-0.002-0.0020.0000.0000.0000.000
175B215PRO00.0140.01630.9750.0070.0070.0000.0000.0000.000
176B216ALA00.0480.00433.113-0.003-0.0030.0000.0000.0000.000
177B217GLU-1-0.857-0.91230.450-0.108-0.1080.0000.0000.0000.000
178B218ALA00.0080.00928.475-0.004-0.0040.0000.0000.0000.000
179B219GLN00.000-0.00329.8650.0000.0000.0000.0000.0000.000
180B220SER0-0.019-0.01331.1080.0030.0030.0000.0000.0000.000
181B221GLY0-0.016-0.02428.392-0.001-0.0010.0000.0000.0000.000
182B222VAL0-0.062-0.01524.235-0.006-0.0060.0000.0000.0000.000
183B223ASP-1-0.874-0.94720.687-0.175-0.1750.0000.0000.0000.000
184B224ASP-1-0.886-0.94717.129-0.296-0.2960.0000.0000.0000.000
185B225VAL0-0.066-0.04820.4300.0210.0210.0000.0000.0000.000
186B226ALA00.0180.00918.878-0.020-0.0200.0000.0000.0000.000
187B227GLY0-0.015-0.00620.8290.0160.0160.0000.0000.0000.000
188B228GLY00.0180.01922.203-0.011-0.0110.0000.0000.0000.000
189B229ILE0-0.072-0.04424.0350.0070.0070.0000.0000.0000.000
190B230PHE0-0.020-0.02927.0150.0080.0080.0000.0000.0000.000
191B231HIS0-0.041-0.01722.8770.0200.0200.0000.0000.0000.000
192B232SER00.0270.01125.105-0.008-0.0080.0000.0000.0000.000
193B233LEU0-0.055-0.03120.2480.0070.0070.0000.0000.0000.000
194B234ALA00.0340.01123.2410.0000.0000.0000.0000.0000.000
195B235LEU0-0.054-0.01218.0970.0010.0010.0000.0000.0000.000
196B236LYS10.9040.95322.1530.1120.1120.0000.0000.0000.000
197B237ASP-1-0.908-0.94023.483-0.133-0.1330.0000.0000.0000.000
198B238GLY0-0.032-0.00520.9330.0060.0060.0000.0000.0000.000
199B239LYS10.7820.86221.9880.1110.1110.0000.0000.0000.000
200B240VAL0-0.0040.00120.642-0.002-0.0020.0000.0000.0000.000
201B241ILE0-0.054-0.02123.4920.0150.0150.0000.0000.0000.000
202B242ALA00.0240.00825.482-0.008-0.0080.0000.0000.0000.000
203B243TRP0-0.055-0.03226.6160.0080.0080.0000.0000.0000.000
204B244GLY00.0560.03529.141-0.006-0.0060.0000.0000.0000.000
205B245ASP-1-0.739-0.85130.623-0.081-0.0810.0000.0000.0000.000
206B246ASN00.0360.01930.251-0.011-0.0110.0000.0000.0000.000
207B247ARG10.8150.89231.7870.0780.0780.0000.0000.0000.000
208B248TYR0-0.053-0.02528.6480.0050.0050.0000.0000.0000.000
209B249LYS10.8930.93227.9790.0740.0740.0000.0000.0000.000
210B250GLN00.0790.03725.858-0.001-0.0010.0000.0000.0000.000
211B251THR00.0230.02125.768-0.009-0.0090.0000.0000.0000.000
212B252THR0-0.099-0.04827.9870.0070.0070.0000.0000.0000.000
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